/*=========================================================================
 *
 *  Copyright UMC Utrecht and contributors
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *        http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#ifndef __elxPCAMetric_HXX__
#define __elxPCAMetric_HXX__

#include "elxPCAMetric.h"
#include "itkTimeProbe.h"

namespace elastix
{

/**
 * ******************* Initialize ***********************
 */

template< class TElastix >
void
PCAMetric< TElastix >
::Initialize( void )
{
  itk::TimeProbe timer;
  timer.Start();
  this->Superclass1::Initialize();
  timer.Stop();
  elxout << "Initialization of PCAMetric metric took: "
         << static_cast< long >( timer.GetMean() * 1000 ) << " ms." << std::endl;

} // end Initialize()


/**
 * ***************** BeforeEachResolution ***********************
 */

template< class TElastix >
void
PCAMetric< TElastix >
::BeforeEachResolution( void )
{
  /** Get the current resolution level. */
  unsigned int level
    = ( this->m_Registration->GetAsITKBaseType() )->GetCurrentLevel();

  unsigned int NumEigenValues = 6;
  this->GetConfiguration()->ReadParameter( NumEigenValues, "NumEigenValues",
    this->GetComponentLabel(), level, 0 );
  this->SetNumEigenValues( NumEigenValues );

  /** Get and set if we want to subtract the mean from the derivative. */
  bool subtractMean = false;
  this->GetConfiguration()->ReadParameter( subtractMean,
    "SubtractMean", this->GetComponentLabel(), 0, 0 );
  this->SetSubtractMean( subtractMean );

  /** Get and set the number of additional samples sampled at the fixed timepoint.  */
//    unsigned int numAdditionalSamplesFixed = 0;
//    this->GetConfiguration()->ReadParameter( numAdditionalSamplesFixed,
//      "NumAdditionalSamplesFixed", this->GetComponentLabel(), level, 0 );
//    this->SetNumAdditionalSamplesFixed( numAdditionalSamplesFixed );

  /** Get and set the fixed timepoint number. */
//    unsigned int reducedDimensionIndex = 0;
//    this->GetConfiguration()->ReadParameter(
//        reducedDimensionIndex, "ReducedDimensionIndex",
//        this->GetComponentLabel(), 0, 0 );
//    this->SetReducedDimensionIndex( reducedDimensionIndex );

  /** Set moving image derivative scales. */
  this->SetUseMovingImageDerivativeScales( false );
  MovingImageDerivativeScalesType movingImageDerivativeScales;
  bool                            usescales = true;
  for( unsigned int i = 0; i < MovingImageDimension; ++i )
  {
    usescales = usescales && this->GetConfiguration()->ReadParameter(
      movingImageDerivativeScales[ i ], "MovingImageDerivativeScales",
      this->GetComponentLabel(), i, -1, true );
  }
  if( usescales )
  {
    this->SetUseMovingImageDerivativeScales( true );
    this->SetMovingImageDerivativeScales( movingImageDerivativeScales );
    elxout << "Multiplying moving image derivatives by: "
           << movingImageDerivativeScales << std::endl;
  }

  /** Check if this transform is a B-spline transform. */
  CombinationTransformType * testPtr1
    = dynamic_cast< CombinationTransformType * >( this->GetElastix()->GetElxTransformBase() );
  if( testPtr1 )
  {
    /** Check for B-spline transform. */
    const BSplineTransformBaseType * testPtr2 = dynamic_cast< const BSplineTransformBaseType * >(
      testPtr1->GetCurrentTransform() );
    if( testPtr2 )
    {
      this->SetGridSize( testPtr2->GetGridRegion().GetSize() );
    }
    else
    {
      /** Check for stack transform. */
      StackTransformType * testPtr3 = dynamic_cast< StackTransformType * >(
        testPtr1->GetModifiableCurrentTransform() );
      if( testPtr3 )
      {
        /** Set itk member variable. */
        this->SetTransformIsStackTransform( true );

        if( testPtr3->GetNumberOfSubTransforms() > 0 )
        {
          /** Check if subtransform is a B-spline transform. */
          const ReducedDimensionBSplineTransformBaseType * testPtr4 = dynamic_cast< const ReducedDimensionBSplineTransformBaseType * >(
            testPtr3->GetSubTransform( 0 ).GetPointer() );
          if( testPtr4 )
          {
            FixedImageSizeType gridSize;
            gridSize.Fill( testPtr3->GetNumberOfSubTransforms() );
            this->SetGridSize( gridSize );
          }
        }
      }
    }
  }
  elxout << "end BeforeEachResolution" << std::endl;

} // end BeforeEachResolution()


} // end namespace elastix

#endif // end #ifndef __elxPCAMetric_HXX__
